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Physical Conditions on Marginal Coral Reefs Thesis submitted by James Christopher WHINNEY MPhys In March 2007 for the degree of Doctor of Philosophy in the School of Mathematics, Physics, and Information Technology James Cook University STATEMENT OF ACCESS I, the undersigned, author of this work, understand that James Cook University will make this thesis available for use within the University Library and, via the Australian Digital Theses network, for use elsewhere. I understand that, as an unpublished work, a thesis has significant protection under the Copyright Act and I do not wish to place any further restriction on access to this work. _________________________ ______________ Signature Date II STATEMENT OF SOURCES DECLARATION I declare that this thesis is my own work and has not been submitted in any form for another degree or diploma at any university or other institution of tertiary education. Information derived from the published or unpublished work of others has been acknowledged in the text and a list of references is given. ____________________________________ ____________________ Signature Date III ELECTRONIC COPY I, the undersigned, the author of this work, declare that the electronic copy of this thesis provided to the James Cook University Library is an accurate copy of the print thesis submitted, within the limits of the technology available. _________________________ ______________ Signature Date IV STATEMENT ON THE CONTRIBUTION OF OTHERS The contributions of others towards this thesis included knowledgeable discussions, proofreading of manuscripts, and manual help with field work. Project costs were covered by the supervisor. Fees and stipend support were paid by an International Postgraduate Research Scholarship and by the School of Mathematics, Physics, and Information Technology. _________________________ ______________ Signature Date V ACKNOWLEDGEMENTS I would like to thank my friends and family for there support during my studies, particularly my wife, Zhen. Thank you to all those people who helped me with my field work and with academic advice, especially my supervisor, Peter Ridd, for his expert advice, guidance and support. VI Abstract The Great Barrier Reef Lagoon (GBRL) is an area of great biodiversity containing 350 species of corals, 10 of which are endemic to the region. In recent years many threats to this ecosystem have been revealed, such as crown-of-thorns starfish and coral bleaching as well as excess concentrations of nutrients and sediments. Information on the effects of water quality and also the amounts of nutrients and sediments that reefs are subjected to is limited. This is especially true for inshore reefs where issues of water quality are most important. This work focuses on the Rockingham Bay and Family Islands region. In this region a reef in Lugger Bay near Mission Beach was selected for a detailed study. It is a highly marginal reef (a reef occurring close to perceived environmental thresholds for coral survival) with high levels of sediments and organic matter and close to the mouths of two rivers: the Tully and the Hull. This makes the reef one of the most at threat from eutrophication and increases in sediment. Part of this work was to document all the physical conditions of the reef including currents, wind speed and direction, light levels, temperature, nutrients, and suspended sediment concentration (SSC). The reef’s health and age were also found by means of photographic surveys and core samples respectively. The main results from the study showed a reef surviving in extreme physical conditions. The SSC on the reef were very high, exceeding 200 mg/l for 28% of the time. Light extinction was common, occurring on 49% of the days that data was recorded. The local rivers did not have much effect on the SSC or nutrient concentrations on the reef. The Tully River only has a wet-season average SSC of 23 mg/l and a maximum of 230 mg/l; resuspension was much more significant. Coral cover on the reef was reasonable, about 57%, and algae only covered 12% of the coral. However, coral species biodiversity was low, with one species of Porites making up 85% of the coral cover. These results indicate that some species of coral are able to survive in areas of high sediment and nutrient concentrations, and that clean rivers in the GBRL are not a great threat to coral reefs. VII The SSC data was also used to develop an empirical model, which predicts SSC for a specific site using just wind data. The model is accurate enough to be used in environmental monitoring to predict an expected SSC, which can be prepared with observed SSC from a site where marine construction is taking place so it can be determined whether the work has increased the SSC to a dangerous level. This makes it an important tool as many such construction projects occur in the GBRL each year and there is no other accurate method of determining what the natural SSC would be if work was not taking place. A new instrument was also developed to infer nutrient concentrations in the water column, to try to overcome problems with existing methods. The instrument works by measuring the speed at which algae grow on a glass plate using a fluorometer. Tests were made to determine how well algal growth would relate to nutrient concentrations, if other factors like temperature, light levels and algal type were not controlled. Results showed that growth was too dependent on these other factors to be a good indicator of nutrient concentrations. The sensor could, however, be used to determine the effect nutrients have on algal growth, which in itself is a potential threat to corals. VIII Table of Contents 1 - Introduction 1 Influences of Nutrients and Sediments in the GBRL 1 Sediment and Nutrient Inputs to the GBRL 1 Sediments 1 Nutrients 3 Potential Impacts of Sediments and Nutrients 5 Sediments 6 Nutrients 7 Thesis Outline 9 Lugger Bay Reef 11 Study Techniques 16 Prediction of SSC 17 Development of an Algal Growth Sensor 18 Thesis Layout 18 2 - Suspended Sediment Concentrations and Fluorescence in an Inshore 20 Reef Region of the Great Barrier Reef Lagoon Abstract 21 Introduction 22 Study Site 26 Methods 29 Data Collection 29 Results 31 SSC and Fluorescence Statistics 31 Temporal Distribution of SSC and Fluorescence Levels 33 Spatial Distribution of SSC and Fluorescence Levels 36 Current Data 37 Discussion 38 Spatial Variation in SSC and Fluorescence 38 Relationship between SSC and Fluorescence 39 Flood Plumes and Wave Resuspension 41 Net Sediment Flow 45 Sediment Input from Outside the Region 46 SSC Levels on the Reefs 46 Conclusion 47 3 - A Case Study of Lugger Bay Reef 53 Abstract 54 Introduction 55 Field Site 56 Methods 58 Results 60 SSC and Light Data 60 Phototransects 63 Core Data 64 Discussion 66 SSC and Light 66 Phototransects 68 IX Coring 69 Conclusion 69 4 - Predicting Suspended Sediment Concentrations on Coral Reefs 73 Using Meteorological Data Abstract 74 Introduction 75 Field Sites 79 Methods 83 SSC Measurements 83 Wind Data 83 Model 84 Kt(twn) – Temporal Wind Weighting Function 85 Wind Direction Weighting Function 87 Tidal effects 88 Model Calibration and Minimisation Function 88 Model Evaluation 89 Results 90 SSC Measurements 90 Model Results 94 Tidal Influence 94 Generated Model Parameters 95 Model Predictions 97 Discussion 105 Conclusion 108 5 - Algal Growth Sensor 111 Abstract 112 Introduction 113 Methods 116 Instrument Design and Construction 116 Instrument Testing 118 Results 119 Discussion 125 Conclusions 128 6 – Conclusions 131 SSC and Fluorescence Throughout the Region 132 Lugger Bay Reef 133 SSC Prediction 134 Algal Growth Sensor 134 Overview 135 7 - Future Work 136 8 - Glossary 137 9 – References 138 X List of Figures Figure 1.1: Fluxes of nitrogen in the Great Barrier Reef Lagoon. 4 Figure 1.2: Reservoirs of nitrogen in the Great Barrier Reef Lagoon. 5 Figure 1.3: Location of Lugger Bay in the North Queensland area. 12 Figure 1.4: Lugger Bay and the surrounding area. 13 Figure 1.5: Photographs of Lugger Bay Reef. 15 Figure 2.1: Location of Lugger Bay and Family Islands region in North 26 Queensland. Figure 2.2: Instrument locations in Lugger Bay and in the surrounding area. 27 Figure 2.3: Box plots of the SSC data. 32 Figure 2.4: Box plots of the fluorescence data. 33 Figure 2.5: Time series of SSC and Fluorescence from 21/12/03 to 34 25/01/04. Figure 2.6: Time series SSC and Fluorescence data from 24/03/04 - 35 28/04/04. Figure 2.7: Longshore current at north of Tully site with a 7 day rolling 38 mean. Figure 2.8: SSC vs. distance from shore for the various sites. 39 Figure 2.9: Correlation between fluorescence and SSC. 40 Figure 2.10: Correlation between SSC and river discharge and between 42 fluorescence and river discharge for Bedarra Island and Lugger Bay Shore. Figure 2.11: Correlation between SSC and Tully River discharge (top), and 43 between SSC and wave height (bottom). Figure 2.12: Correlation between fluorescence and SSC during Tully River 45 high and low discharge events for SSC events of over 200 mg/l for Lugger Bay Shore. Figure 3.1: Location of Lugger Bay Reef in the North Queensland region. 57 Figure 3.2: Photographs of Lugger Bay Reef. 58 Figure 3.3: Diagram of Lugger Bay Reef with the three instrument sites, 59 four percussion core sites and two phototransects shown. Figure 3.4: Box plots of SSC data from the three Lugger Bay instrument 61 sites. Figure 3.5: Light and SSC time series for Lugger Bay. 62 Figure 3.6: Example sections of the phototransects. 64 Figure 3.7: Phototransect analysis.

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